Cargando…

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae ge...

Descripción completa

Detalles Bibliográficos
Autores principales:	Goodwin, Sara, Gurtowski, James, Ethe-Sayers, Scott, Deshpande, Panchajanya, Schatz, Michael C., McCombie, W. Richard
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2015
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617970/ https://www.ncbi.nlm.nih.gov/pubmed/26447147 http://dx.doi.org/10.1101/gr.191395.115

Ejemplares similares

Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2
por: Mak, Q X Charles, et al.
Publicado: (2023)

Hybrid error correction and de novo assembly of single-molecule sequencing reads
por: Koren, Sergey, et al.
Publicado: (2012)

Current challenges in de novo plant genome sequencing and assembly
por: Schatz, Michael C, et al.
Publicado: (2012)

Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
por: Mikheenko, Alla, et al.
Publicado: (2022)

Optimized use of Oxford Nanopore flowcells for hybrid assemblies
por: Lipworth, Samuel, et al.
Publicado: (2020)

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION
por: Leija‐Salazar, Melissa, et al.
Publicado: (2019)

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens
por: Deschamps, Stéphane, et al.
Publicado: (2016)

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies
por: Ammer-Herrmenau, Christoph, et al.
Publicado: (2021)

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
por: Dutreux, Fabien, et al.
Publicado: (2018)

Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm
por: Wang, Jinming, et al.
Publicado: (2021)

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica
por: Schatz, Michael C, et al.
Publicado: (2014)

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
por: Holley, Guillaume, et al.
Publicado: (2021)

Oxford Nanopore MinION Sequencing and Genome Assembly
por: Lu, Hengyun, et al.
Publicado: (2016)

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
por: Istace, Benjamin, et al.
Publicado: (2017)

Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing
por: Huang, Yao-Ting, et al.
Publicado: (2021)

High resolution copy number inference in cancer using short-molecule nanopore sequencing
por: Baslan, Timour, et al.
Publicado: (2021)

Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
por: Geng, Keyi, et al.
Publicado: (2022)

The use of Oxford Nanopore native barcoding for complete genome assembly
por: Bayliss, Sion C, et al.
Publicado: (2017)

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing
por: Dhar, Ruby, et al.
Publicado: (2019)

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly
por: Tan, Mun Hua, et al.
Publicado: (2018)

Hybrid-hybrid correction of errors in long reads with HERO
por: Kang, Xiongbin, et al.
Publicado: (2023)

Hybrid assembly with long and short reads improves discovery of gene family expansions
por: Miller, Jason R., et al.
Publicado: (2017)

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing
por: Chen, Zhao, et al.
Publicado: (2020)

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
por: Yang, Rendong, et al.
Publicado: (2015)

nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples
por: Liou, Ci-Hong, et al.
Publicado: (2020)

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing
por: Wick, Ryan R., et al.
Publicado: (2023)

Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
por: Sutton, John M., et al.
Publicado: (2021)

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing
por: Erkes, Annett, et al.
Publicado: (2023)

Ray Meta: scalable de novo metagenome assembly and profiling
por: Boisvert, Sébastien, et al.
Publicado: (2012)

De novo assembly of viral quasispecies using overlap graphs
por: Baaijens, Jasmijn A., et al.
Publicado: (2017)

Accurate long-read de novo assembly evaluation with Inspector
por: Chen, Yu, et al.
Publicado: (2021)

Haploflow: strain-resolved de novo assembly of viral genomes
por: Fritz, Adrian, et al.
Publicado: (2021)

Assisted assembly: how to improve a de novo genome assembly by using related species
por: Gnerre, Sante, et al.
Publicado: (2009)

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
por: Sahlin, Kristoffer, et al.
Publicado: (2021)

HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing
por: Han, Renmin, et al.
Publicado: (2023)

Evaluation of de novo transcriptome assemblies from RNA-Seq data
por: Li, Bo, et al.
Publicado: (2014)

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
por: Haas, Brian J, et al.
Publicado: (2008)

Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding
por: Freed, Nikki E, et al.
Publicado: (2020)

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes
por: Davidson, Nadia M, et al.
Publicado: (2014)

TransRate: reference-free quality assessment of de novo transcriptome assemblies
por: Smith-Unna, Richard, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_v443ms4oon57td5ba260nqlgjb